College of Liberal Arts & Sciences
CCG Center Equipment
Applied Biosystems 3500 Genetic Analyzer
The ABI 3500 Genetic Analyzer is an 8-capillary DNA sequencer and genotyper that provides automated genetic analysis of DNA fragments. The instrument is fully automated from sample loading through data analysis. The 3500 is used for DNA fragment analysis such as microsatellites, SNP analysis, mutation detection, and Sanger Sequencing of plasmids and PCR products.
https://tools.thermofisher.com/content/sfs/brochures/3500-Genetic-Analyzer-Specification-Sheet.pdf
Applied Biosystems QuantStudio 3
The Applied Biosystems QuantStudio 3 system for real-time PCR is capable of running 96 samples. Its fixed block accommodates 0.1ml sample plates, and has 3 VeriFlex temperature control zones. It can handle multiplexing of up to 4 targets. The user-friendly interface of QuantStudio Design and Analysis software makes it easy to set up your reaction. The software can also perform a variety of automated standard or custom analyses, or you can export raw data.
Agilent BioAnalyzer 2100
The Agilent BioAnalyzer 2100 is an automated capillary electrophoresis system used to evaluate the quality of a sample containing DNA, RNA, or proteins. It uses a microfluidics system, which greatly reduces the amount of sample required for analysis as compared to traditional electrophoresis. This is a full-service machine.
Bio-Rad Experion Automated Electrophoresis Station
The Bio-Rad Experion Automated Electrophoresis Station is a microfluidics-based electrophoresis system. The Experion is used to assess the quality of RNA. The output consists of a virtual agarose gel of the RNA, a graphical representation of the relative fluorescence, and a numerical RNA quality, integrity score.
View Example Output from Experion Automated Electrophoresis Station
Bio-Rad QX200 Droplet Digital PCR System
The QX200 Droplet Digital PCR (ddPCR) System provides absolute quantification of target DNA or RNA molecules for EvaGreen or probe-based digital PCR applications. The system consists of two instruments, the QX200 Droplet Generator and the QX200 Droplet Reader, and their associated consumables. The QX200 Droplet Generator is used to partition ddPCR reaction mix into thousands of nanoliter-sized droplets. After PCR on a thermal cycler, droplets from each sample are analyzed individually on the QX200 Droplet Reader. Droplets are ready well by well as they are streamed single file past a two-color optical detection system in a serial manner. Up to 96 samples can be processed per run. The QX200 Droplet Digital PCR System requires use of the C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module and the PX1 PCR Plate Sealer. All of these instruments are available in the Carver Center for Genomics (CCG). For benefits and applications of the QX200 Droplet Digital PCR System and additional information, please click on this link.
Additional files and training materials provided by Bio-Rad can be downloaded.
BioTek® Cytation 5
The Cytation 5 is a combination microscope and plate reader. The instrument accommodates a wide range of plate formats (including microscope slides). The user programs the instrument to perform automated imaging of fields within specified wells. A laser auto-focus system calibrates the objective for the optimal focal plane which preserves high image quality and consistency. With three objectives (4X, 10X, 20X), users can visualize whole organisms (ex: zebrafish larva, nematodes) or subcellular compartments (ex: mitochondria). The instrument possesses three filter cubes (DAPI, GFP, and Texas Red) as well as the capacity to detect UV/Vis absorbance, luminescence, and programs to quantify DNA/RNA. The system also regulates temperature/CO2 to permit long-term imaging (potentially over several days) under controlled environmental conditions. Image analysis software (Gen5TM Image Prime) facilitates automated quantification of images.
Additional information can be found with this link below:
https://www.biotek.com/products/imaging-microscopy-cell-imaging-multi-mode-readers/cytation-5-cell-imaging-multi-mode-reader/
Illumina iSeq 100
The Illumina iSeq is a benchtop sequencer that can generate 1.2Gb of data in only 17.5 hours. This machine is ideal for small NGS projects, such as small genome sequencing, targeted sequencing, or small panels. The library preps for the iSeq are identical to the NovaSeq, which means the iSeq can also be used to check the balance of pooled libraries before running a large project on the NovaSeq 6000.
Invitrogen Qubit 4
This all-in-one fluorometer by Invitrogen can perform rapid and highly accurate assays to quantitate nucleic acids, proteins, or ion sphere particles in a sample. The Qubit can measure nucleic acids with as little as 0.1 ng added to the assay. The proprietary Qubit nucleic acid assays require only two standards, which come premixed to reduce error, and there are pre-set protocols in the machine to use with these kits. The Qubit can also run on fluorometer mode using nucleic acid-binding fluorescent dyes such as PicoGreen or RiboGreen, where the user can set up an appropriate range and number of standards suited to their samples.
LI-COR® Odyssey Classic Infrared Imaging System
The LI-COR® Odyssey Classic Infrared Imaging System is a laser-based imager used to detect and quantify fluorescence signals for Near-infrared Fluorescent Western Blots, In-Gel Western Assays, In-Cell Western Assays, Electrophoretic Mobility Shift Assays, RNAi Analysis, Tissue Section Imaging, Reporter Gene Assays, and Nucleic Acid Gel Documentation. This instrument is equipped with two infrared channels allowing one to probe two separate targets in the same experiments or use the second channel for normalization.
LI-COR® Odyssey Fc Dual Mode Imaging System
The LI-COR® Odyssey Fc Dual Mode Infrared System is a CCD-based imager that features two solid state laser diodes (685 and 785 nm) and a low-noise CCD camera for detection of two channel near-infrared fluorescence and chemiluminescent signals. Applications include: Western Blots (chemiluminescent, two-color infrared, and in-gel), protein detection (Coomassie-stained gels), and nucleic acid detection (SYBR-family stains). For scan documentation and data analysis, the system uses the Image Studio Software.
Molecular Devices SpectraMax M2 Microplate Reader
The SpectraMax M2 is a multi-detection microplate reader – UV-Vis absorbance, luminescence, and fluorescence intensity. Assays can be performed using standard cuvettes or microplates (6 to 384 well). The system can be used for endpoint, kinetic, spectrum, area-well scanning, and full spectral range detection. Bottom read fluorescence is available for cell-based assays.
Qiagen TissueLyser LT
The Qiagen TissueLyser LT is a small bead mill that provides fast, effective disuption of up to 12 samples at the same time. Simultaneous disruption and homogenization is achieved through high-speed shaking of samples in 2 ml microcentrifuge tubes with stainless steel or glass beads.
Sage Science BluePippin
The BluePippin from Sage Science is an automated DNA size fractionator, enabling isolation of specific size ranges of DNA fragments from a sample. This machine performs electrophoresis on 4-5 samples in parallel using separate lanes of a cartridge, eliminating the possibility of cross contamination that can occur when cutting bands out of a gel. The BluePippin elutes the targeted fragments in buffer, so no additional gel extraction protocol is required. Used as part of a workflow for NGS, the BluePippin can result in a significantly higher proportion of reads of the desired length.
Spectronics SpectroLinker XL1000
The XL1000 is designed to monitor UV radiation and self-adjust to variations in UV intensity. All Spectroline UV crosslinkers feature a "smart" microprocessor controller and unique true UV monitoring circuitry to enable users to get error-free results with speed, accuracy, and safety. Covalently binds nucleic acid sequences and hybridization membranes in 30 seconds or less. Ensures optimum nucleic acid membrane binding even when UV output varies.
Thermal Cycler - Eppendorf MasterCycler Pro (2 units)
The Eppendorf MasterCycler Pro features an easy-to-use interface with graphical programming, SteadySlope gradient technology, Vapo-protect lid technology, fast heating (4 C/second) and cooling (3 C/second) rates, and block uniformity of +/- 0.4 C. The gradient option of the MasterCycler Pro features SteadySlope technology to ensure that the heating and cooling ramp rates are identical in both gradient and normal operation. Thus, you can expect identical temperature control characteristics in both optimization and routine experiments. Vapo-protect lid technology is used to reduce evaporation and increase reproducibility.
Thermo Scientific NanoDrop One Spectrophotometer
The NanoDrop One is a spectrophotometer that allows for measurement of only 1.5 ul of sample. The instrument is used to measure the concentrations of nucleic acids (dsDNA, ssDNA, RNA, oligo DNA, oligo RNA, and labeled DNA for microarray) and protein (A280, A205, BCA Bradford, Lowry, and Pierce 660). The software includes Acclaro Sample Intelligence technology with the measurements of each sample, which can help with contaminant identification. Output includes the sample concentration and the 260/280 and 260/230 ratios in a table format. Users also have the option of downloading the raw data to recreate the plot of the spectral scan.
UVP UVsolo touch – Gel Documentation
The UVP UVsolo touch is a compact, easy-to-use, stand-alone system for gel documentation. It is designed to acquire gel images easily and without any need for training. Thus, it is ideal for multi-user laboratories and practical trainings. The system is controlled by a touch screen with intuitive image acquisition software. The main application of the UVP UVsolo touch is saving and printing gel images. VisionWorks software allows for gel analysis.
Decommissioned Equipment
ABI 3730 DNA Analyzer (Decommissioned October 2021)
The ABI 3730 DNA Analyzer is a 48-capillary DNA sequencer and genotyper that provides automated high throughput genetic analysis of DNA fragments. The 3730 can sequence 48 samples in parallel in two hours providing the capacity for analyzing hundreds of DNA samples per day. The instrument is fully automated from sample loading through data analysis. The 3730 is used for DNA fragment analysis such as microsatellites, SNP analysis, mutation detection, and Sanger Sequencing of plasmids and PCR products.
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Roche LightCycler® 480 Real-Time PCR System (Decommissioned October 2021)
The CCG has the Roche 480 Real-time PCR instrument that can run 96 samples at once. The instrument offers users the choice of different fluorescent probes and multiplicity of the PCR target within the same reaction. Currently, this instrument is being used for sample quantification and genotyping analyses.
Thermal Cycler - GeneStorm GS-4 (Decommissioned 2021)
The GeneStorm GS-4 thermal cycler contains 4 independently controlled 96 well blocks. Features include user selectable variable-temperature heated lids, heating/cooling ramping speed of 3C/sec, gradient temperature range of 30 - 80 C, touch-screen and keyboard/mouse control, and drag and drop programming.
Turner BioSystems TBS-380 Fluorometer (Decommissioned November 2021)
The TBS-380 Fluorometer is a mini-fluorometer that is capable of accurately measuring extremely low concentrations of nucleic acids – dsDNA as low as 1 ng/ml in a PicoGreen assay, RNA as low as 1 ng/ml in a RiboGreen assay. Unlike spectrophotometers, the TBS-380 when used in conjunction with PicoGreen or RiboGreen is relatively insensitive to proteins, free nucleotides, and reagent contaminants generally found in DNA and RNA preparations. When used with minicell cuvettes, measurements can be carried out in as little as 50 ul.
